Final Report Summary - PRIMATESVS (Identification and characterization of primate structural variation and an assessment of intra-specific patterns of selection and copy-number variation)
After the characterization of thousand of human genomes, primates (our closest relatives) are still kind of forgotten. Most genome projects included only one individual as a reference but in order to understand the impact of genomic variation in the evolution of every species we need to include polymorphisms data into the equation. We can only understand the origins of genomic variants and phenotypical differences among species if we can model variation within species and compare it to a proper perspective with the differences among species.
In my lab we have leaded the most comprehensive analysis to understand the evolution of human genomic variation in the last 15 million years, by comparing the diversity of all great apes to human populations. To this end, we have sequenced and analyzed 80 great ape genomes sequenced at high coverage, finding novel relationships among them and providing a new perspective to their population dynamics.
In particular, our work is a significant advance over the previously knowledge in terms of comparing human diversity in an evolutionary context. We provided what is today the most complete catalog of great ape variation showing drastic differences in population history between human and great apes. We found extensive inbreeding in almost all wild populations, with eastern gorillas being the most extreme. Also, we characterized loss-of-function variants in the human lineages and conclude that the rate of gene loss has not been different in the human branch compared to other branches in the great ape phylogeny. We also have showed that CNV diversity partially correlates with SNP diversity and that current patterns of human CNVs were not created in a linear mode in the last 15 Myrs, but there was a burst of duplications at the time of the common ancestor of African great apes. In contrast the rate of deletions in the great ape phyllogeny has been more constant in time. Finally, we have showed that a substantial fraction of human duplications have had a recent acceleration in the rate of protein coding evolution of the genes embedded within them.
In my lab we have leaded the most comprehensive analysis to understand the evolution of human genomic variation in the last 15 million years, by comparing the diversity of all great apes to human populations. To this end, we have sequenced and analyzed 80 great ape genomes sequenced at high coverage, finding novel relationships among them and providing a new perspective to their population dynamics.
In particular, our work is a significant advance over the previously knowledge in terms of comparing human diversity in an evolutionary context. We provided what is today the most complete catalog of great ape variation showing drastic differences in population history between human and great apes. We found extensive inbreeding in almost all wild populations, with eastern gorillas being the most extreme. Also, we characterized loss-of-function variants in the human lineages and conclude that the rate of gene loss has not been different in the human branch compared to other branches in the great ape phylogeny. We also have showed that CNV diversity partially correlates with SNP diversity and that current patterns of human CNVs were not created in a linear mode in the last 15 Myrs, but there was a burst of duplications at the time of the common ancestor of African great apes. In contrast the rate of deletions in the great ape phyllogeny has been more constant in time. Finally, we have showed that a substantial fraction of human duplications have had a recent acceleration in the rate of protein coding evolution of the genes embedded within them.